Job ID = 12265997 SRX = SRX7282631 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19835 spots for SRR10603134/SRR10603134.sra Written 19835 spots for SRR10603134/SRR10603134.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266105 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:02 19835 reads; of these: 19835 (100.00%) were unpaired; of these: 2340 (11.80%) aligned 0 times 9129 (46.02%) aligned exactly 1 time 8366 (42.18%) aligned >1 times 88.20% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 10077 / 17495 = 0.5760 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:42:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 08:42:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:42:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:33: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:42:33: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:42:33: #1 total tags in treatment: 7418 INFO @ Sat, 03 Apr 2021 08:42:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:42:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:42:33: #1 tags after filtering in treatment: 7417 INFO @ Sat, 03 Apr 2021 08:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:42:33: #1 finished! INFO @ Sat, 03 Apr 2021 08:42:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:42:33: #2 number of paired peaks: 223 WARNING @ Sat, 03 Apr 2021 08:42:33: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 03 Apr 2021 08:42:33: start model_add_line... INFO @ Sat, 03 Apr 2021 08:42:33: start X-correlation... INFO @ Sat, 03 Apr 2021 08:42:33: end of X-cor INFO @ Sat, 03 Apr 2021 08:42:33: #2 finished! INFO @ Sat, 03 Apr 2021 08:42:33: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:42:33: #2 alternative fragment length(s) may be 9,63,100,122,153,183,208,230,265,283,295,317,405,553 bps INFO @ Sat, 03 Apr 2021 08:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05_model.r WARNING @ Sat, 03 Apr 2021 08:42:33: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:42:33: #2 You may need to consider one of the other alternative d(s): 9,63,100,122,153,183,208,230,265,283,295,317,405,553 WARNING @ Sat, 03 Apr 2021 08:42:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:42:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:42:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.05_summits.bed INFO @ Sat, 03 Apr 2021 08:42:33: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:43:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 08:43:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:43:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:43:03: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:43:03: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:43:03: #1 total tags in treatment: 7418 INFO @ Sat, 03 Apr 2021 08:43:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:43:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:43:03: #1 tags after filtering in treatment: 7417 INFO @ Sat, 03 Apr 2021 08:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:43:03: #1 finished! INFO @ Sat, 03 Apr 2021 08:43:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:43:03: #2 number of paired peaks: 223 WARNING @ Sat, 03 Apr 2021 08:43:03: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 03 Apr 2021 08:43:03: start model_add_line... INFO @ Sat, 03 Apr 2021 08:43:03: start X-correlation... INFO @ Sat, 03 Apr 2021 08:43:03: end of X-cor INFO @ Sat, 03 Apr 2021 08:43:03: #2 finished! INFO @ Sat, 03 Apr 2021 08:43:03: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:43:03: #2 alternative fragment length(s) may be 9,63,100,122,153,183,208,230,265,283,295,317,405,553 bps INFO @ Sat, 03 Apr 2021 08:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10_model.r WARNING @ Sat, 03 Apr 2021 08:43:03: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:43:03: #2 You may need to consider one of the other alternative d(s): 9,63,100,122,153,183,208,230,265,283,295,317,405,553 WARNING @ Sat, 03 Apr 2021 08:43:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:43:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:43:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:43:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:43:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.10_summits.bed INFO @ Sat, 03 Apr 2021 08:43:03: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 03 Apr 2021 08:43:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:43:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:43:33: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:43:33: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:43:33: #1 total tags in treatment: 7418 INFO @ Sat, 03 Apr 2021 08:43:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:43:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:43:33: #1 tags after filtering in treatment: 7417 INFO @ Sat, 03 Apr 2021 08:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:43:33: #1 finished! INFO @ Sat, 03 Apr 2021 08:43:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:43:33: #2 number of paired peaks: 223 WARNING @ Sat, 03 Apr 2021 08:43:33: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 03 Apr 2021 08:43:33: start model_add_line... INFO @ Sat, 03 Apr 2021 08:43:33: start X-correlation... INFO @ Sat, 03 Apr 2021 08:43:33: end of X-cor INFO @ Sat, 03 Apr 2021 08:43:33: #2 finished! INFO @ Sat, 03 Apr 2021 08:43:33: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:43:33: #2 alternative fragment length(s) may be 9,63,100,122,153,183,208,230,265,283,295,317,405,553 bps INFO @ Sat, 03 Apr 2021 08:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20_model.r WARNING @ Sat, 03 Apr 2021 08:43:33: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:43:33: #2 You may need to consider one of the other alternative d(s): 9,63,100,122,153,183,208,230,265,283,295,317,405,553 WARNING @ Sat, 03 Apr 2021 08:43:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:43:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:43:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282631/SRX7282631.20_summits.bed INFO @ Sat, 03 Apr 2021 08:43:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling